Rare Variants in 48 Genes Account for 42% of Cases of Epilepsy With or Without Neurodevelopmental Delay in 246 Pediatric Patients

Abstract

In order to characterize the genetic architecture of epilepsy in a pediatric population from the Iberian Peninsula (including the Canary Islands), we conducted targeted exome sequencing of 246 patients with infantile-onset seizures with or without neurodevelopmental delay. We detected 107 variants in 48 different genes, which were implicated in neuronal excitability, neurodevelopment, synaptic transmission, and metabolic pathways. In 104 cases (42%) we detected variant(s) that we classified as pathogenic or likely pathogenic. Of the 48 mutated genes, 32 were dominant, 8 recessive and 8 X-linked. Of the patients for whom family studies could be performed and in whom pathogenic variants were identified in dominant or X-linked genes, 82% carried de novo mutations. The involvement of small copy number variations (CNVs) is 9%. The use of progressively updated custom panels with high mean vertical coverage enabled establishment of a definitive diagnosis in a large proportion of cases (42%) and detection of CNVs (even duplications) with high fidelity. In 10.5% of patients we detected associations that are pending confirmation via functional and/or familial studies. Our findings had important consequences for the clinical management of the probands, since a large proportion of the cohort had been clinically misdiagnosed, and their families were subsequently able to avail of genetic counseling. In some cases, a more appropriate treatment was selected for the patient in question, or an inappropriate treatment discontinued. Our findings suggest the existence of modifier genes that may explain the incomplete penetrance of some epilepsy-related genes. We discuss possible reasons for non-diagnosis and future research directions. Further studies will be required to uncover the roles of structural variants, epimutations, and oligogenic inheritance in epilepsy, thereby providing a more complete molecular picture of this disease. In summary, given the broad phenotypic spectrum of most epilepsy-related genes, efficient genomic tools like the targeted exome sequencing panel described here are essential for early diagnosis and treatment, and should be implemented as first-tier diagnostic tools for children with epilepsy without a clear etiologic basis.

Keywords: de novo mutations; epilepsy; genetic diagnosis; incomplete penetrance; modifier genes; neurodevelopmental disorders.

Figure 1

Z-score for each gene in Table 1, calculated as described in the section Material and Methods. AD, autosomal dominant inheritance; AR, autosomal recessive inheritance; X-linked: X-linked inheritance.

Figure 2

(A,B) Boxplot showing GERP/CONDEL scores (median and interquartile range) for missense variants. Scores for the pathogenic missense variants reported in Table 1 are shown in red, and scores for the missense variants found in control samples within each gene are shown in yellow. Only genes with pathogenic missense variants are shown. Genes with autosomal dominant inheritance (AD) are shown in blue, genes with autosomal recessive inheritance (AR) in red, and genes with X-linked inheritance in green.

Figure 3

Proportions of different types of inheritance (A), different types of variants (B), and the proportion of de novo events for the Iberian epilepsy cohort (C).

Figure 4

Locations of variants found in our cohort in the proteins encoded by the following genes: (A) SCN1A; (B) SCN2A; (C) KCNQ2; (D) KCNA2; (E) KCNB1; (F) KCNT1; (G) HCN1.

Figure 5

Locations of variants found in our cohort in the following genes: (A) ARX; (B) MECP2; (C) FOXG1; (D) CDKL5; (E) ARHGEF9; (F) DNM1; (G) SYN1; (H) GRIN2A; (I) RhoBTB2; (J) MTOR. NTD, N-terminal domain; MBD, methyl CpG binding domain; TRD, transcriptional repression domain; NLS, nuclear localization signal; CTD, C-terminal domain; FHD, forkhead domain.

Figure 6

Microdeletions found in RBFOX1 and GPHN. Yellow, (Lionel et al., 2013); green, (Dejanovic et al., 2014); blue, Fernández-Marmiesse (present study).